Does Septra cause diarrhea? Understanding the Side Effects of This Antibiotic

October 12, 2025 •

4 min read

About 1 in 5 people who take antibiotics experience antibiotic-associated diarrhea, a common side effect of many antibacterial medications. So, does Septra cause diarrhea? Yes, it is a known and frequent side effect of this medication.

Quick Summary

Septra (sulfamethoxazole/trimethoprim) can cause diarrhea by disrupting the balance of healthy gut bacteria. While often mild, persistent or bloody diarrhea could indicate a more serious infection with C. difficile. Management includes staying hydrated and consulting a doctor before using anti-diarrheal medication.

Key Points

Diarrhea is a Common Side Effect: Septra (sulfamethoxazole/trimethoprim) frequently causes diarrhea, as do many other antibiotics, by disrupting the balance of gut flora.
C. difficile is a Serious Risk: In some cases, Septra can lead to an overgrowth of C. difficile, a bacteria that causes severe, watery, or bloody diarrhea and requires immediate medical attention.
Stay Hydrated and Eat a Bland Diet: For mild diarrhea, focus on rehydration with water and electrolytes, and consume easy-to-digest foods like bananas, rice, and toast.
Avoid Antidiarrheals Unless Advised: Do not take over-the-counter anti-diarrheal medications without a doctor's approval, as they can worsen a C. difficile infection.
Contact Your Doctor for Severe Symptoms: Seek immediate medical help if you experience severe, persistent, or bloody diarrhea, fever, or abdominal cramps.
Probiotics May Help: Some evidence suggests that probiotics can help restore gut bacteria balance and potentially reduce the risk of antibiotic-associated diarrhea, but consult a doctor first.

What is Septra?

Septra is a brand name for a combination antibiotic containing sulfamethoxazole and trimethoprim. It is used to treat a variety of bacterial infections, including urinary tract infections, respiratory infections like bronchitis, and certain intestinal infections. As with most antibiotics, its mechanism of action—killing harmful bacteria—can also affect the beneficial bacteria residing in your gut. This disruption of the natural balance of gut flora, known as the microbiome, is the primary reason for antibiotic-associated diarrhea.

The Mechanism Behind Septra-Induced Diarrhea

When you take an antibiotic, it doesn't just target the specific bacteria causing your infection. It can also eliminate some of the 'good' bacteria in your digestive system that are crucial for healthy digestion. This creates an imbalance that can lead to several gastrointestinal issues, with diarrhea being one of the most common.

How does this affect your gut?

Flora Disruption: The normal, healthy bacteria in the colon help break down food and keep harmful pathogens in check. When Septra kills off these good bacteria, it allows bad bacteria to thrive.
Clostridioides difficile (C. diff) Risk: A more severe complication of this imbalance is an overgrowth of a specific bacterium called Clostridioides difficile (C. diff). C. diff produces toxins that can cause severe, watery, or bloody diarrhea, fever, and stomach cramps. This can occur during treatment or even weeks after stopping Septra.

Managing Mild Diarrhea from Septra

For many people, the diarrhea caused by Septra is mild and resolves once the course of medication is finished. However, even mild cases should be managed to prevent dehydration and discomfort.

Here are some steps you can take:

Stay Hydrated: Drink plenty of water and fluids containing electrolytes, such as broths or sports drinks, to replace lost fluids.
Follow a Bland Diet: The BRAT diet (bananas, rice, applesauce, toast) is often recommended, as these foods are easy to digest. Avoiding dairy products, fatty foods, and spicy meals can also help.
Consider Probiotics: Some studies suggest that taking probiotic supplements or eating probiotic-rich foods like yogurt or kefir may help restore the balance of healthy gut bacteria and reduce the risk of antibiotic-associated diarrhea. It is best to consult your doctor before starting a probiotic regimen.
Avoid Anti-Diarrheal Medications: Unless instructed by a doctor, you should not take over-the-counter anti-diarrheal medications like loperamide. These can trap toxins in the body, which is particularly dangerous if the diarrhea is caused by C. diff.

When to Contact a Healthcare Provider

While mild diarrhea is a common side effect, certain symptoms warrant immediate medical attention. Contact your doctor or seek emergency care if you experience any of the following:

Severe or persistent diarrhea: Defined as three or more watery stools a day for more than two days.
Bloody or black, tarry stools: This can be a sign of a more serious intestinal issue.
Severe abdominal pain or cramping: Intense pain in the belly area can indicate a more serious problem.
Fever: A new fever accompanied by diarrhea could signal an infection like C. diff.
Signs of Dehydration: Symptoms include little to no urination, intense thirst, dizziness, or weakness.

Comparison of Diarrhea Risk with Common Antibiotics

Different types of antibiotics carry varying risks of causing diarrhea. The following table provides a general comparison based on documented side effect profiles, but individual reactions can vary significantly. Some antibiotics, like clindamycin, are notorious for their high risk of causing C. difficile infections.


Antibiotic Class	Examples	Relative Risk of Diarrhea	Notes
Sulfa Drug (e.g., Septra)	Sulfamethoxazole/Trimethoprim	Moderate	Common side effect; can lead to C. diff overgrowth.
Penicillins	Amoxicillin, Ampicillin	Moderate to High	High incidence, especially with amoxicillin-clavulanate.
Cephalosporins	Cefdinir, Cephalexin	Moderate to High	Frequently implicated in antibiotic-associated diarrhea.
Fluoroquinolones	Ciprofloxacin, Levofloxacin	Moderate to High	A known risk factor for C. difficile infection.
Macrolides	Clarithromycin, Clindamycin	High	Clindamycin has a particularly high association with C. difficile.

Conclusion

In conclusion, does Septra cause diarrhea? Yes, it is a common side effect, as it can disrupt the natural bacterial balance in your gut. For many, this is a temporary and mild issue. However, it is crucial to monitor symptoms closely. If diarrhea is severe, bloody, or accompanied by fever and cramping, it could be a sign of a more serious infection, and you should contact a healthcare provider immediately. Staying hydrated and following a bland diet can help manage mild symptoms, but never take anti-diarrheal medication without consulting your doctor. Proper antibiotic use and awareness of potential side effects are key to ensuring a safe recovery.

For more information on antibiotic-associated diarrhea, consult the Mayo Clinic's guide.

Frequently Asked Questions

Yes, diarrhea is a common side effect of Septra and other antibiotics. It occurs because the medication disrupts the natural balance of beneficial bacteria in your digestive system, leading to gastrointestinal upset.

Mild diarrhea is typically less severe and resolves on its own or shortly after stopping the antibiotic. A C. difficile infection, however, can cause severe, watery or bloody stools, fever, and severe abdominal cramping, and may appear weeks after treatment.

To help prevent diarrhea, some people use probiotic supplements or consume probiotic-rich foods like yogurt to help restore gut bacteria. Staying hydrated and maintaining a healthy diet are also important.

You should call your doctor if you experience severe, bloody, or watery diarrhea that lasts more than two days. Other red flags include a new fever, severe abdominal pain, or signs of dehydration.

No, you should not take an anti-diarrheal medication without first checking with your doctor. These medications can interfere with your body's ability to clear harmful toxins, especially if you have a C. difficile infection.

In addition to diarrhea, Septra can cause other gastrointestinal side effects such as nausea, vomiting, loss of appetite, and abdominal pain.

Mild antibiotic-associated diarrhea often resolves within a few days of completing the antibiotic course. However, if it is caused by C. difficile, it can be more persistent and require specific treatment.